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2026 Vol.39, Issue 4 Preview Page
SNP-Based Analysis of Genetic Population Structure and IBS-Based Identification of Cultivar-Related Genetic Resources in Rice Germplasm

SNP 기반 벼 유전자원의 유전적 집단구조 분석 및 IBS를 이용한 육성품종 근연 자원 탐색

Hyeon Park1†
,
Sang-Ho Chu2†
,
Yong-Jin Park3†
,
Hee-Jong Woo4
,
Ho Cheol Ko4
,
Young-ah Jeon4
,
Yuna Kang5
,
Bichsaem Kim5
,
Dong Su Yu5
박 현1†
,
추 상호2†
,
박 용진3†
,
우 희종4
,
고 호철4
,
전 영아4
,
강 유나5
,
김 빛샘5
,
유 동수5
1Post-doc, National Institute of Agricultural Sciences, RDA, Wanju 55365, Korea
2Research Professor, Department of Plant Resources, Kongju National University, Yesan 32439, Korea
3Professor, Department of Plant Resources, Kongju National University, Yesan 32439, Korea
4Senior Researcher, National Institute of Agricultural Sciences, RDA, Wanju 55365, Korea
5Researcher, National Institute of Agricultural Sciences, RDA, Wanju 55365, Korea
1농촌진흥청 국립농업과학원, 박사후연구원
2국립공주대학교 식물자원학과, 연구교수
3국립공주대학교 식물자원학과, 교수
4농촌진흥청 국립농업과학원, 연구관
5농촌진흥청 국립농업과학원, 연구사
*Corresponding Author
†These authors contributed equally to this work.
1 August 2026. pp. 203-213
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Abstract

Rice (Oryza sativa L.) is a major staple crop worldwide, and the effective use of diverse genetic resources is essential for developing climate-resilient cultivars. In this study, 1,418 rice accessions representing cultivars, landraces, indica-type weedy rice, and wild rice groups were genotyped using the 580K_KNU chip, and 22,950 high-quality SNP markers were used to evaluate genetic diversity and identify germplasm for further evaluation. Genetic diversity analysis revealed substantial genome-wide variation in minor allele frequency (MAF), expected heterozygosity (He), observed heterozygosity (Ho), and polymorphism information content (PIC). Population structure inferred from ADMIXTURE and principal coordinates analysis (PCoA) showed clear genetic differentiation among the five populations, further supported by Fst estimates indicating that weedy rice exhibited the greatest genetic divergence. Identity-by-state (IBS) analysis identified accessions genetically closest to nine cultivars. Six cultivars were predominantly associated with landrace accessions, while the remaining three exhibited closer genetic proximity to indica-type weedy rice accessions. These results likely reflect differences in breeding history and genetic backgrounds among cultivar groups, and the selected accessions can be proposed as priority candidates for subsequent phenotypic evaluation. Overall, this study provides a comprehensive genetic characterization of Korean rice germplasm and highlights priority germplasm candidates for future phenotypic evaluation and rice improvement programs.

Keywords
Genetic diversity
Plant genetic resource
Rice
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Information
  • Publisher :The Plant Resources Society of Korea
  • Publisher(Ko) :한국자원식물학회
  • Journal Title :Korean Journal of Plant Resources
  • Journal Title(Ko) :한국자원식물학회지
  • Volume : 39
  • No :4
  • Pages :203-213
  • Received Date : 2026-05-13
  • Revised Date : 2026-06-09
  • Accepted Date : 2026-06-22
  • DOI :https://doi.org/10.7732/kjpr.2026.39.4.203
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